A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly

Abstract

A hallmark of histone H3 lysine 9 (H3K9) methylated heterochromatin, conserved from fission yeast,Schizosaccharomyces pombe (S. pombe), to humans, is its ability to spread to adjacent genomic regions1–6. Central to heterochromatin spread is the heterochromatin protein 1 (HP1), which recognizes H3K9 methylated chromatin, oligomerizes, and forms a versatile platform that participates in diverse nuclear functions, ranging from gene silencing to chromosome segregation1–6. How HP1 proteins assemble on methylated nucleosomal templates and how the HP1-nucleosome complex achieves functional versatility remain poorly understood. Here, we show that binding of the major S. pombe HP1 protein, Swi6, to methylated nucleosomes drives a switch from an auto-inhibited state to a spreading competent state. In the auto-inhibited state, a histone mimic sequence in one Swi6 monomer blocks methyl mark recognition by the chromodomain of another monomer. Auto-inhibition is relieved by recognition of two template features, the H3K9 methyl mark and nucleosomal DNA. Cryo-Electron Microscopy (EM) based reconstruction of the Swi6-nucleosome complex provides the overall architecture of the spreading-competent state in which two unbound chromodomain sticky ends appear exposed. Disruption of the switch between the auto-inhibited and spreading competent state disrupts heterochromatin assembly and gene silencing in vivo. These findings are reminiscent of other conditionally activated polymerization processes, such as actin nucleation, and open up a new class of regulatory mechanisms that operate on chromatin in vivo.

Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles

“…Careful biophysical characterization has previously allowed the elucidation of isodemic self‐association behavior for several other proteins, including insulin (Jeffrey et al , 1976), FtsZ (Rivas et al , 2000), Phage ϕ29 protein p6 (Abril et al , 1997), chicken deoxy hemoglobin D (Rana & Riggs, 2011), human apolipoprotein C‐II (Yang et al , 2012), tubulin (Frigon & Timasheff, 1975), and for the assembly of heterochromatin protein 1 with nucleosomes in controlling heterochromatin spread (Canzio et al , 2013). Isodesmic self‐association may be a general mechanism for creating large, labile polymers that can disaggregate readily when required.…”

“…Some of these assemblies form via nucleation‐driven polymerization and result in stable complexes, and we are starting to understand the structural basis for their proximity‐enhanced activation (Korennykh et al , 2009; Yin et al , 2009; Li et al , 2012a; Lu et al , 2014). Other assemblies depend on transient interactions and are more labile, generating oligomers with broad size distributions (Rivas et al , 2000; Errington et al , 2012; Canzio et al , 2013). The functions of these more labile higher‐order oligomers are not well understood.…”

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

“…In several areas of chromosome biology, researchers assume the existence of a tight coupling between 3D chromatin structure and epigenetic dynamics, as this coupling provides an appealing mechanism for the de novo establishement and maintainance of epigenetic patterns [38,40,46,47,49]. However, as both epigenetic spreading and chromatin dynamics may occur on comparable and relatively fast timescales in vivo (minutes to hours [20,68]), it is extremely difficult to design an experiment to demonstrate this coupling dynamically inside the cell.…”

“…These two latter quantities are the main free parameters of the system: the stretching force f can be controlled in vitro through either optical or magnetic tweezers, while the binding affinity between readers and epigenetic marks may be varied by considering mutants of bridging proteins such as HP1 [36,46].…”

Touch, act and go: landing and operating on nucleosomes

“…Many of these techniques make use of fluorescence, which overcomes limitations of dynamic range posed by other techniques, such as isothermal calorimetry, that is however successfully employed for the analysis of nucleosome-derived peptides. Among these fluorescence-based techniques, we find fluorescence polarization (FP), a versatile in-solution method that allows quantitative and rapid analysis of molecular interactions (Eryilmaz et al, 2009;Lea & Simeonov, 2011;Rossi & Taylor, 2011;Canzio et al, 2013;Al-Ani et al, 2014a;Mattiroli et al, 2014;Pilotto et al, 2015;Taherbhoy et al, 2015). Microscale thermophoresis (MST) also takes advantage of fluorescence detection in solution to measure molecular interactions in a flexible and rapid manner (Schubert et al, 2012;Greer et al, 2014;Zhang et al, 2014).…”